https://speakerdeck.com/jennybc/googlesheets-talk-at-user2015
install.packages("googlesheets")
library(googlesheets)https://docs.google.com/spreadsheets/d/1WBrH655fxqKW1QqvD5hnqvvEWIvRzDJcKEgjjFeYxeM/edit#gid=0
sheets_url = paste0("https://docs.google.com/spreadsheets/d/",
"1WBrH655fxqKW1QqvD5hnqvvEWIvRzDJcKEgjjFeYxeM")
gsurl1 = gs_url(sheets_url)
Warning: `as_data_frame()` is deprecated as of tibble 2.0.0. Please use `as_tibble()` instead. The signature and semantics have changed, see `?as_tibble`. This warning is displayed once every 8 hours. Call `lifecycle::last_warnings()` to see where this warning was generated.
dat = gs_read(gsurl1) date_read = lubridate::today() head(dat)
# A tibble: 6 x 12
Git Github R Rstudio `Reproducible R… `R markdown` `Data import`
<dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 9 9 9 9 9 9 10
2 1 1 5 5 7 5 4
3 0 0 2 3 3 0 3
4 0 1 1 1 1 1 1
5 0 2 7 7 7 5 8
6 2 2 3 2 0 0 1
# … with 5 more variables: `Web scraping` <dbl>, `Data cleaning` <dbl>,
# dplyr <dbl>, Bioconductor <dbl>, `Regular expressions` <dbl>
library(googlesheets4) # May be necessary on rstudio.cloud options(httr_oob_default=TRUE) # Will ask you to log in out = read_sheet(sheets_url)
token = readr::read_rds("googledrive_token.rds")
library(googledrive)
drive_auth(token = token) # could also use googlesheets4::gs4_auth
library(googlesheets4)
out = read_sheet(sheets_url)
head(out)
# A tibble: 6 x 12
Git Github R Rstudio `Reproducible R… `R markdown` `Data import`
<dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 9 9 9 9 9 9 10
2 1 1 5 5 7 5 4
3 0 0 2 3 3 0 3
4 0 1 1 1 1 1 1
5 0 2 7 7 7 5 8
6 2 2 3 2 0 0 1
# … with 5 more variables: `Web scraping` <dbl>, `Data cleaning` <dbl>,
# dplyr <dbl>, Bioconductor <dbl>, `Regular expressions` <dbl>
#install.packages("jsonlite")
library(jsonlite)
jsonData <- fromJSON("https://api.github.com/users/jtleek/repos")
head(jsonData)
id node_id name
1 155565363 MDEwOlJlcG9zaXRvcnkxNTU1NjUzNjM= 2018
2 264786491 MDEwOlJlcG9zaXRvcnkyNjQ3ODY0OTE= ads2020
3 101394164 MDEwOlJlcG9zaXRvcnkxMDEzOTQxNjQ= advdatasci
4 111447948 MDEwOlJlcG9zaXRvcnkxMTE0NDc5NDg= advdatasci-project
5 47568815 MDEwOlJlcG9zaXRvcnk0NzU2ODgxNQ== advdatasci-swirl
6 41645119 MDEwOlJlcG9zaXRvcnk0MTY0NTExOQ== advdatasci15
full_name private owner.login owner.id owner.node_id
1 jtleek/2018 FALSE jtleek 1571674 MDQ6VXNlcjE1NzE2NzQ=
2 jtleek/ads2020 FALSE jtleek 1571674 MDQ6VXNlcjE1NzE2NzQ=
3 jtleek/advdatasci FALSE jtleek 1571674 MDQ6VXNlcjE1NzE2NzQ=
4 jtleek/advdatasci-project FALSE jtleek 1571674 MDQ6VXNlcjE1NzE2NzQ=
5 jtleek/advdatasci-swirl FALSE jtleek 1571674 MDQ6VXNlcjE1NzE2NzQ=
6 jtleek/advdatasci15 FALSE jtleek 1571674 MDQ6VXNlcjE1NzE2NzQ=
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6 https://api.github.com/users/jtleek/orgs
owner.repos_url
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3 https://api.github.com/users/jtleek/repos
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owner.events_url
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owner.received_events_url owner.type
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4 https://api.github.com/users/jtleek/received_events User
5 https://api.github.com/users/jtleek/received_events User
6 https://api.github.com/users/jtleek/received_events User
owner.site_admin html_url
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2 FALSE https://github.com/jtleek/ads2020
3 FALSE https://github.com/jtleek/advdatasci
4 FALSE https://github.com/jtleek/advdatasci-project
5 FALSE https://github.com/jtleek/advdatasci-swirl
6 FALSE https://github.com/jtleek/advdatasci15
description
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2 Advanced Data Science 2020 Edition
3 <NA>
4 Awesome project!
5 <NA>
6 Advanced Data Science @ JHU Biostats
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3 TRUE https://api.github.com/repos/jtleek/advdatasci
4 FALSE https://api.github.com/repos/jtleek/advdatasci-project
5 FALSE https://api.github.com/repos/jtleek/advdatasci-swirl
6 FALSE https://api.github.com/repos/jtleek/advdatasci15
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pulls_url
1 https://api.github.com/repos/jtleek/2018/pulls{/number}
2 https://api.github.com/repos/jtleek/ads2020/pulls{/number}
3 https://api.github.com/repos/jtleek/advdatasci/pulls{/number}
4 https://api.github.com/repos/jtleek/advdatasci-project/pulls{/number}
5 https://api.github.com/repos/jtleek/advdatasci-swirl/pulls{/number}
6 https://api.github.com/repos/jtleek/advdatasci15/pulls{/number}
milestones_url
1 https://api.github.com/repos/jtleek/2018/milestones{/number}
2 https://api.github.com/repos/jtleek/ads2020/milestones{/number}
3 https://api.github.com/repos/jtleek/advdatasci/milestones{/number}
4 https://api.github.com/repos/jtleek/advdatasci-project/milestones{/number}
5 https://api.github.com/repos/jtleek/advdatasci-swirl/milestones{/number}
6 https://api.github.com/repos/jtleek/advdatasci15/milestones{/number}
notifications_url
1 https://api.github.com/repos/jtleek/2018/notifications{?since,all,participating}
2 https://api.github.com/repos/jtleek/ads2020/notifications{?since,all,participating}
3 https://api.github.com/repos/jtleek/advdatasci/notifications{?since,all,participating}
4 https://api.github.com/repos/jtleek/advdatasci-project/notifications{?since,all,participating}
5 https://api.github.com/repos/jtleek/advdatasci-swirl/notifications{?since,all,participating}
6 https://api.github.com/repos/jtleek/advdatasci15/notifications{?since,all,participating}
labels_url
1 https://api.github.com/repos/jtleek/2018/labels{/name}
2 https://api.github.com/repos/jtleek/ads2020/labels{/name}
3 https://api.github.com/repos/jtleek/advdatasci/labels{/name}
4 https://api.github.com/repos/jtleek/advdatasci-project/labels{/name}
5 https://api.github.com/repos/jtleek/advdatasci-swirl/labels{/name}
6 https://api.github.com/repos/jtleek/advdatasci15/labels{/name}
releases_url
1 https://api.github.com/repos/jtleek/2018/releases{/id}
2 https://api.github.com/repos/jtleek/ads2020/releases{/id}
3 https://api.github.com/repos/jtleek/advdatasci/releases{/id}
4 https://api.github.com/repos/jtleek/advdatasci-project/releases{/id}
5 https://api.github.com/repos/jtleek/advdatasci-swirl/releases{/id}
6 https://api.github.com/repos/jtleek/advdatasci15/releases{/id}
deployments_url
1 https://api.github.com/repos/jtleek/2018/deployments
2 https://api.github.com/repos/jtleek/ads2020/deployments
3 https://api.github.com/repos/jtleek/advdatasci/deployments
4 https://api.github.com/repos/jtleek/advdatasci-project/deployments
5 https://api.github.com/repos/jtleek/advdatasci-swirl/deployments
6 https://api.github.com/repos/jtleek/advdatasci15/deployments
created_at updated_at pushed_at
1 2018-10-31T13:50:37Z 2018-10-31T13:50:41Z 2018-10-30T18:13:41Z
2 2020-05-18T00:45:46Z 2020-06-27T15:14:17Z 2020-05-22T22:16:49Z
3 2017-08-25T10:38:16Z 2020-07-13T14:18:23Z 2020-05-17T23:06:04Z
4 2017-11-20T18:33:29Z 2017-11-20T18:35:50Z 2017-11-20T18:40:45Z
5 2015-12-07T17:43:53Z 2018-04-30T21:02:30Z 2015-12-09T20:21:13Z
6 2015-08-30T22:27:26Z 2019-12-06T08:56:59Z 2015-12-16T18:12:31Z
git_url
1 git://github.com/jtleek/2018.git
2 git://github.com/jtleek/ads2020.git
3 git://github.com/jtleek/advdatasci.git
4 git://github.com/jtleek/advdatasci-project.git
5 git://github.com/jtleek/advdatasci-swirl.git
6 git://github.com/jtleek/advdatasci15.git
ssh_url
1 git@github.com:jtleek/2018.git
2 git@github.com:jtleek/ads2020.git
3 git@github.com:jtleek/advdatasci.git
4 git@github.com:jtleek/advdatasci-project.git
5 git@github.com:jtleek/advdatasci-swirl.git
6 git@github.com:jtleek/advdatasci15.git
clone_url
1 https://github.com/jtleek/2018.git
2 https://github.com/jtleek/ads2020.git
3 https://github.com/jtleek/advdatasci.git
4 https://github.com/jtleek/advdatasci-project.git
5 https://github.com/jtleek/advdatasci-swirl.git
6 https://github.com/jtleek/advdatasci15.git
svn_url
1 https://github.com/jtleek/2018
2 https://github.com/jtleek/ads2020
3 https://github.com/jtleek/advdatasci
4 https://github.com/jtleek/advdatasci-project
5 https://github.com/jtleek/advdatasci-swirl
6 https://github.com/jtleek/advdatasci15
homepage size stargazers_count watchers_count
1 https://jhu-advdatasci.github.io/2018/ 60855 0 0
2 <NA> 12 32 32
3 <NA> 172184 17 17
4 <NA> 680 0 0
5 <NA> 188 4 4
6 <NA> 200992 14 14
language has_issues has_projects has_downloads has_wiki has_pages forks_count
1 HTML FALSE TRUE TRUE TRUE FALSE 2
2 <NA> TRUE TRUE TRUE TRUE FALSE 3
3 HTML FALSE TRUE TRUE TRUE TRUE 8
4 HTML TRUE TRUE TRUE TRUE FALSE 0
5 HTML TRUE TRUE TRUE TRUE FALSE 2
6 HTML TRUE TRUE TRUE TRUE TRUE 7
mirror_url archived disabled open_issues_count license.key license.name
1 NA FALSE FALSE 0 <NA> <NA>
2 NA FALSE FALSE 0 <NA> <NA>
3 NA FALSE FALSE 0 <NA> <NA>
4 NA FALSE FALSE 0 <NA> <NA>
5 NA FALSE FALSE 1 <NA> <NA>
6 NA FALSE FALSE 0 <NA> <NA>
license.spdx_id license.url license.node_id forks open_issues watchers
1 <NA> <NA> <NA> 2 0 0
2 <NA> <NA> <NA> 3 0 32
3 <NA> <NA> <NA> 8 0 17
4 <NA> <NA> <NA> 0 0 0
5 <NA> <NA> <NA> 2 1 4
6 <NA> <NA> <NA> 7 0 14
default_branch
1 master
2 master
3 master
4 master
5 master
6 gh-pages
dim(jsonData)
[1] 30 73
head(jsonData$name)
[1] "2018" "ads2020" "advdatasci" [4] "advdatasci-project" "advdatasci-swirl" "advdatasci15"
class(jsonData$owner) #Some of the columns is a data frame!
[1] "data.frame"
dim(jsonData$owner); names(jsonData$owner)
[1] 30 18
[1] "login" "id" "node_id" [4] "avatar_url" "gravatar_id" "url" [7] "html_url" "followers_url" "following_url" [10] "gists_url" "starred_url" "subscriptions_url" [13] "organizations_url" "repos_url" "events_url" [16] "received_events_url" "type" "site_admin"
Chrome:
Firefox:
right click on page
select “view source” Microsoft Edge:
right click on page
select “view source”
Safari
https://cran.r-project.org/web/packages/rvest/vignettes/selectorgadget.html
recount_url = "http://bowtie-bio.sourceforge.net/recount/"
# install.packages("rvest")
library(rvest)
htmlfile = read_html(recount_url)
nds = html_nodes(htmlfile,
xpath='//*[@id="recounttab"]/table')
dat = html_table(nds)
dat = as.data.frame(dat)
head(dat)
X1 X2 X3
1 Study PMID Species
2 bodymap not published, but publicly available here human
3 cheung 20856902 human
4 core 19056941 human
5 gilad 20009012 human
6 maqc 20167110 human
X4 X5
1 Number of biological replicates Number of uniquely aligned reads
2 19 2,197,622,796
3 41 834,584,950
4 2 8,670,342
5 6 41,356,738
6 14 (technical)** 2 (biological) 71,970,164
X6 X7 X8
1 ExpressionSet Count table Phenotype table
2 link link link
3 link link link
4 link link link
5 link link link
6 original pooled original pooled original pooled
X9
1 Notes
2 Illumina Human BodyMap 2.0 -- tissue comparison
3 HapMap - CEU
4 lung fibroblasts
5 liver; males and femlaes
6 experiment: MAQC-2
colnames(dat) = as.character(dat[1,]) dat = dat[-1,] head(dat)
Study PMID Species
2 bodymap not published, but publicly available here human
3 cheung 20856902 human
4 core 19056941 human
5 gilad 20009012 human
6 maqc 20167110 human
7 montgomery 20220756 human
Number of biological replicates Number of uniquely aligned reads
2 19 2,197,622,796
3 41 834,584,950
4 2 8,670,342
5 6 41,356,738
6 14 (technical)** 2 (biological) 71,970,164
7 60 *886,468,054
ExpressionSet Count table Phenotype table
2 link link link
3 link link link
4 link link link
5 link link link
6 original pooled original pooled original pooled
7 link link link
Notes
2 Illumina Human BodyMap 2.0 -- tissue comparison
3 HapMap - CEU
4 lung fibroblasts
5 liver; males and femlaes
6 experiment: MAQC-2
7 HapMap - CEU
http://motherboard.vice.com/read/70000-okcupid-users-just-had-their-data-published
https://www.theguardian.com/science/2012/may/23/text-mining-research-tool-forbidden
http://www.ncbi.nlm.nih.gov/books/NBK25501/
https://ropensci.org/packages/
https://docs.github.com/en/rest/reference/repos
https://docs.github.com/en/rest/reference/rate-limit
https://api.github.com/search/repositories?q=created:2014-08-13+language:r+-user:cran
https://api.github.com/search/repositories?q=created:2014-08-13+language:r+-user:cran
q parameterhttps://api.github.com/search/repositories?q=created:2014-08-13+language:r+-user:cran
https://api.github.com/search/repositories?q=created:2014-08-13+language:r+-user:cran
https://api.github.com/search/repositories?q=created:2014-08-13+language:r+-user:cran
#install.packages("httr")
library(httr)
query_url = paste0("https://api.github.com/", "search/repositories",
"?q=created:2014-08-13", "+language:r", "+-user:cran")
req = GET(query_url)
names(content(req))
[1] "total_count" "incomplete_results" "items"
(see also twitteR package)
myapp = oauth_app("twitter",
key="yourConsumerKeyHere",secret="yourConsumerSecretHere")
sig = sign_oauth1.0(myapp,
token = "yourTokenHere",
token_secret = "yourTokenSecretHere")
homeTL = GET("https://api.twitter.com/1.1/statuses/home_timeline.json", sig)
# But you can get cool data
json1 = content(homeTL)
json2 = jsonlite::fromJSON(toJSON(json1))
json2[1,1:4]
created_at id id_str
1 Mon Jan 13 05:18:04 +0000 2014 4.225984e+17 422598398940684288
text
1 Now that P. Norvig's regex golf IPython notebook hit Slashdot, let's see if our traffic spike tops the previous one: http://t.co/Vc6JhZXOo8